In order to analyze the complex chemical kinetic mechanism systematically and find out the redundant species and reactions, a numerical platform for mechanism analysis and simplification is established basing on Path ...In order to analyze the complex chemical kinetic mechanism systematically and find out the redundant species and reactions, a numerical platform for mechanism analysis and simplification is established basing on Path Flux Analysis （PFA）. It is used to reduce a detailed mechanism for flame inhibited by phosphorus containing compounds, a reduced mechanism with 65 species and 335 reactions is obtained. The detailed and reduced mechanism are both used to calculate the freely-propagating premix C3H8/air flame with different dimethyl methylphosphonate doped over a wide range of equivalence ratios. The concentration distributions of free radicals and major species are compared, and the results under two different mechanisms agree well. The laminar flame speed obtained by the two mechanisms also matches well, with the maximum relative error introduces as a small value of 1.7%. On the basis of the reduced mechanism validation, the correlativity analysis is conducted between flame speed and flee radical concentrations, which can provide information for target species selection in the further mechanism reduction. By analyzing the species and reactions fluxes, the species and reaction paths which contribute the flame inhibition significantly are determined.展开更多
Reduced graphene oxide is the precursor to produce graphene in a large scale;however,to date,there has been no consensus on the electronic structure of reduced graphene oxide.In this study,we carried out an ab initio ...Reduced graphene oxide is the precursor to produce graphene in a large scale;however,to date,there has been no consensus on the electronic structure of reduced graphene oxide.In this study,we carried out an ab initio molecular dynamics simulation to investigate the adsorption process of hydroxyl groups on graphene surface.During the adsorption process,the OH group needs to firstly pass through a physical adsorption complex with the OH above the bridge site of two carbon atoms,next to surmount a transition state,then to be adsorbed at the atop site of a carbon atom.With a 5×5 graphene surface,up to 6 hydroxyl groups can be adsorbed on the graphene surface,indicating the concentration coverage of the hydroxyl groups on graphene surface is about 12%.The simulation results show that the negative adsorption energy increases linearly as the number of adsorbed hydroxyl groups increases,and the band gap also increases linearly with the number of adsorbed hydroxyl groups.展开更多
The two-dimensional barrier passage is studied in the framework of Langevin statistical reactive dynamics.The optimal incident angle for a particle diffusing in the dissipative non-orthogonal environment with various ...The two-dimensional barrier passage is studied in the framework of Langevin statistical reactive dynamics.The optimal incident angle for a particle diffusing in the dissipative non-orthogonal environment with various strengthsof coupling between the two degrees of freedom is systematically calculated.The optimal diffusion path of the particlein a non-Ohmic damping system is revealed to have a probability to return to the potential valley under the combinedinfluence of the off-diagonal system tensors.展开更多
We describe a computational approach,incorporating quantum mechanics into enzyme kinetics modeling with a special emphasis on computation of kinetic isotope effects.Two aspects are highlighted:(1) the potential energy...We describe a computational approach,incorporating quantum mechanics into enzyme kinetics modeling with a special emphasis on computation of kinetic isotope effects.Two aspects are highlighted:(1) the potential energy surface is represented by a combined quantum mechanical and molecular mechanical(QM/MM) potential in which the bond forming and breaking processes are modeled by electronic structure theory,and(2) a free energy perturbation method in path integral simulation is used to determine both kinetic isotope effects(KIEs).In this approach,which is called the PI-FEP/UM method,a light(heavy) isotope is mutated into a heavy(light) counterpart in centroid path integral simulations.The method is illustrated in the study of primary and secondary KIEs in two enzyme systems.In the case of nitroalkane oxidase,the enzymatic reaction exhibits enhanced quantum tunneling over that of the uncatalyzed process in water.In the dopa delarboxylase reaction,there appears to be distinguishable primary carbon-13 and secondary deuterium KIEs when the internal proton tautomerism is in the N-protonated or in the O-protonated positions.These examples show that the incorporation of quantum mechanical effects in enzyme kinetics modeling offers an opportunity to accurately and reliably model the mechanisms and free energies of enzymatic reactions.展开更多
基金Project supported by the National Natural Science Foundation of China(Nos.51178427 and 51278451)the National Basic Research Program(973 Program)of China(No.2014CB047005)
基金Supported by the National Natural Science Foundation of China （51176181）, the National Basic Research Program of China （2012CB719704）, and the Research Fund for the Doctoral Program of Higher Education （20123402110047）.
文摘In order to analyze the complex chemical kinetic mechanism systematically and find out the redundant species and reactions, a numerical platform for mechanism analysis and simplification is established basing on Path Flux Analysis （PFA）. It is used to reduce a detailed mechanism for flame inhibited by phosphorus containing compounds, a reduced mechanism with 65 species and 335 reactions is obtained. The detailed and reduced mechanism are both used to calculate the freely-propagating premix C3H8/air flame with different dimethyl methylphosphonate doped over a wide range of equivalence ratios. The concentration distributions of free radicals and major species are compared, and the results under two different mechanisms agree well. The laminar flame speed obtained by the two mechanisms also matches well, with the maximum relative error introduces as a small value of 1.7%. On the basis of the reduced mechanism validation, the correlativity analysis is conducted between flame speed and flee radical concentrations, which can provide information for target species selection in the further mechanism reduction. By analyzing the species and reactions fluxes, the species and reaction paths which contribute the flame inhibition significantly are determined.
基金supported by the National Natural Science Foundation of China(No.11774206)Taishan Scholarship Fund from Shandong Province。
文摘Reduced graphene oxide is the precursor to produce graphene in a large scale;however,to date,there has been no consensus on the electronic structure of reduced graphene oxide.In this study,we carried out an ab initio molecular dynamics simulation to investigate the adsorption process of hydroxyl groups on graphene surface.During the adsorption process,the OH group needs to firstly pass through a physical adsorption complex with the OH above the bridge site of two carbon atoms,next to surmount a transition state,then to be adsorbed at the atop site of a carbon atom.With a 5×5 graphene surface,up to 6 hydroxyl groups can be adsorbed on the graphene surface,indicating the concentration coverage of the hydroxyl groups on graphene surface is about 12%.The simulation results show that the negative adsorption energy increases linearly as the number of adsorbed hydroxyl groups increases,and the band gap also increases linearly with the number of adsorbed hydroxyl groups.
基金Supported by the Scientific Research Starting Foundation of Qufu Normal University and the National Natural Science Foundation of China under Grant No.10847101
文摘The two-dimensional barrier passage is studied in the framework of Langevin statistical reactive dynamics.The optimal incident angle for a particle diffusing in the dissipative non-orthogonal environment with various strengthsof coupling between the two degrees of freedom is systematically calculated.The optimal diffusion path of the particlein a non-Ohmic damping system is revealed to have a probability to return to the potential valley under the combinedinfluence of the off-diagonal system tensors.
基金supported in part by the National Institutes of Health (GM46736)
文摘We describe a computational approach,incorporating quantum mechanics into enzyme kinetics modeling with a special emphasis on computation of kinetic isotope effects.Two aspects are highlighted:(1) the potential energy surface is represented by a combined quantum mechanical and molecular mechanical(QM/MM) potential in which the bond forming and breaking processes are modeled by electronic structure theory,and(2) a free energy perturbation method in path integral simulation is used to determine both kinetic isotope effects(KIEs).In this approach,which is called the PI-FEP/UM method,a light(heavy) isotope is mutated into a heavy(light) counterpart in centroid path integral simulations.The method is illustrated in the study of primary and secondary KIEs in two enzyme systems.In the case of nitroalkane oxidase,the enzymatic reaction exhibits enhanced quantum tunneling over that of the uncatalyzed process in water.In the dopa delarboxylase reaction,there appears to be distinguishable primary carbon-13 and secondary deuterium KIEs when the internal proton tautomerism is in the N-protonated or in the O-protonated positions.These examples show that the incorporation of quantum mechanical effects in enzyme kinetics modeling offers an opportunity to accurately and reliably model the mechanisms and free energies of enzymatic reactions.
